1918 H1N1 Viral influenza polymerase heterotrimer - Endonuclease and priming loop ordered (Class2a)

2024-07-10 REL PDBe PDBe PDBe 2021-02-10 2021-12-01 2021-12-01 2024-07-10 Wellcome Trust 200835/Z/16/Z United Kingdom Medical Research Council (MRC, United Kingdom) MR/R009945/1 United Kingdom Medical Research Council (MRC, United Kingdom) MR/K000241/1 United Kingdom 1918 H1N1 Viral influenza polymerase heterotrimer - Endonuclease and priming loop ordered (Class2a) Keown JR Carrique L Influenza, RNA polymerase, H1N1, 1918, VIRAL PROTEIN Keown JR Zhu Z Carrique L Fan H Walker AP Serna Martin I Pardon E Steyaert J Fodor E Grimes JM Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies. Nat Commun UK 13 251 251 2022 35017564 doi:10.1038/s41467-021-27950-w 2041-1723 7nha FULLOVERLAP 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters 0 1 2 3 1918 Influenza virus polymerase 1 1 2 3 Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) vRNA promoters 1 4 5 synthetic construct Polymerase acidic protein Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) A/Brevig Mission/1/1918 H1N1 0.082707391 1 Spodoptera frugiperda LEVO MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINERGESIIVESGDPNALLKHRFEIIE GRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKAD YTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNG YIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMRTFFGWKEP NVVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNMKKTSQLKWALGENMAPEKVDFDDCKDVSDLKQYDSDEPEL RSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDF QLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRSAIGQVSRP MFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTL LAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR Q3HM39 3.1.-.- RNA-directed RNA polymerase catalytic subunit Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) A/Brevig Mission/1/1918 H1N1 0.086625211 1 Spodoptera frugiperda LEVO MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGRWTTNTETGAPQLNPIDGPLPEDNEPS GYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES GRLIDFLKDVMESMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA IATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLA MITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLASIDLKYFNDSTRKKIEKIRPLLIDGT ASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLLGINMSKK KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYR CHRGDTQIQTRRSFEIKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESV NNAVMMPAHGPAKNMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK Q3HM40 2.7.7.48 Polymerase basic protein 2,Immunoglobulin G-binding protein A Staphylococcus aureus 0.10237721899999999 1 Spodoptera frugiperda LEVO MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSK TNDAGSDRVMVSPLAVTWWNRNGPTTSAVHYPKIYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQ DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKISPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRIS SSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSMRGVRV SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEVNGPESVLVNTYQWIIRNWETV KIQWSQNPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNV RGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDRRYGPALSINELSNLAKGE KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINENLYFQGELKTAALAQHDEAVDNKFNKEQQNAFYEILHLPN LNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKADPSQSAN LLAEAKKLNGAQAPKVDANSAGKST Q3HM41 P38507 RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') synthetic construct 0.005335125 1 GGCCUGCUUUUGCUAUU RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') synthetic construct 0.004862017 1 AGUAGAAACAAGGCC singleParticle particle 0.3 7.5 25.0 NaSCN Sodium thiocynate 20.0 HEPES-Na HEPES 166.0 NaCl Sodium Chloride 0.0075 Tween 20 Quantifoil R2/1 COPPER 200 GLOW DISCHARGE 30 AIR ETHANE 100 298 FEI VITROBOT MARK IV

3.5 second blot and 3 microlitres sample..

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1 9413 5.0 61.5 1 2854501

Initial automated blob picking followed by template picking.

C1 2.91 FSC 0.143 CUT-OFF cryoSPARC 2.15 144328 RANDOM ASSIGNMENT cryoSPARC 2.15 MAXIMUM LIKELIHOOD cryoSPARC 2.15

Non-uniform refinement

emd_12322.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.2 211.2 211.2 90.0 90.0 90.0 X Y Z -0.20692647 0.49333924 0.001729485 0.0181855 0.825 0.825 0.825 0.0505 AUTHOR ::::EMDATABANK.org::::EMD-12322::::